Updates

Model and report changes

  1. The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly since the outset of the Survey in May 2020 for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths.
  2. The model now accounts for the ongoing immunisation programme, stratifying the population of people still susceptible to infection with the virus according to their immunisation status (unimmunised/1 dose/2 doses). We use data on the daily proportions of the population getting immunised to inform this splitting of the population, assuming that it takes three weeks for vaccine-derived immunity to develop .
  3. The geographical definition has been changed from the seven NHS regions (map) to the nine regions typically used in government (map). This new spatial definition more appropriately reflects the existing regional heterogeneity.
  4. Using observations of improved survival in hospitalised COVID-19 patients, we have allowed the probability of dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) to gradually change over the course of June 2020, with a decrease being estimated. More recently, the Kent variant of the virus has gradually become the predominant virus strain and we accordingly allow for a change in the IFR over the period in which the relative prevalence of this strain has been growing.
  5. The ‘Epidemic summary’ now only reports the current value for the IFR by age. To visualise how this has changed over time in our model, see the IFR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of dying if infected, taking into account the impact of the immunisation programme.
  6. The modelling now accounts for a different susceptibility to infection in the under-15s, using information from literature (Viner et al, 2020) suggesting that children less likely to acquire infection when in contact with an infectious individual.

Updated findings

  1. The current estimate of the daily number of new infections occurring each day across England is 3,840 (2,510–5,9430, 95% credible interval).
  2. The daily infection rate is estimated to be the highest in London (GL) with 783, new daily infections, corresponding to 9 per 100,000 population per day. All other regions have 6–7 new infections per 100k population with the exception of the North West where incidence appears low. Note these regional estimates are highly uncertain and that a substantial proportion of these daily infections will be asymptomatic.
  3. We predict that the number of deaths occurring daily is likely to remain low with a forecast for the period around the 28th May suggesting that there will be between 9 and 35 deaths per day.
  4. The probability of Rt exceeding 1 is 70% and 67% in the South West (SW) and GL respectively; 59% in both the East of England (EE) and South East (SE); around 30% in the West and East Midlands (WM and EM), North East (NE) and Yorkshire and Humber (YH); and less than 5% in the NW.
  5. The growth rate for England remains at 0.01 (-0.01–0.03, 95% credible interval) per day. This means that, nationally, the number of infections is likely to be increasing, although there is considerable uncertainty and heterogeneity across regions, with negative growth in many, the NW in particular.
  6. London, followed by the WM and the NE, have the highest attack rates, that is the proportions of the regional populations who have ever been infected, with 32%, 21% and 20% respectively. The SW continues to have the lowest attack rate at 10%. These constitute a big downward revision from our previous published report, particularly so for the NW.
  7. Note that the deaths data used are only very weakly informative on Rt over the last two weeks and are thankfully becoming increasingly sparse. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to some revision.

Interpretation

The plots of the estimated Rt in the most recent weeks are heavily influenced by the effects of the reopening of schools following the Easter holidays and the gradual relaxation of pandemic mitigation measures. Going forward, however, as restrictions continue to be relaxed, we anticipate Rt to remain stable. The Rt for four regions have central estimates just above 1 (EE, GL, SE, SW), although these estimates are uncertain. At current levels of incidence, these values of Rt are not a particular concern, though they do require careful monitoring.

The incidence of deaths has continued to fall more sharply than predicted by the model and is anticipated to continue to fall for the coming three weeks, despite the number of new infections, as the Rt values indicate, remaining flat in almost all regions.

The plot of the infection fatality rate (IFR) presents age-specific probabilities of death given infection. It shows an increasing mortality risk from September onwards in all ages until the immunisation programme begins to have an impact in late January. From the end of January we estimate a decreasing IFR in all adult age groups, but most steeply in the older ages. This drop measures the benefits of immunisation against death over and above the benefits against infection. Specifically, there is an estimated fall to a still-high 15% in the over-75s and 0.35% overall. The overall impact of the immunisation programme can be seen more clearly in the ‘All Ages’ plot, where the precipitous decline in IFR since late January is a product of this efficacy against death but also of the increasing proportion of infections in young people as older age groups are immunised and become protected against infection. The impact of the second immunisation doses becoming widespread will begin to affect this quantity over the coming weeks.

Estimates of cumulative infection are low in comparison to some earlier reports. This is due to the inclusion of the prevalence data, which appear to have the effect of reducing the number of infections. Nowhere is this more true than in the North West, where estimates of attack rate have fallen to 17%. London remains the region with the largest levels of cumulative infection to date.

Other indicators (e.g. hospital bed prevalence, reported new cases) continue to suggest a declining epidemic. Prevalence of infection, as estimated by the ONS Community Infections Survey is now around 0.10% in England with some regional heterogeneity. It is hoped that these trends continue, enabling the continued progressive relaxation of pandemic mitigation measures in line with the government’s roadmap to opening society. We will continue to monitor the situation closely.

Summary

Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.

Methods

We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.

Data sources

We use:

  1. Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing This consists of a combination of deaths notified to:
    • the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
    • NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
    • Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020)
  2. Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors.

Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).

  1. Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
  2. Information on contacts between different age groups from:
    • A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
    • Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
    • The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
    • Data from the Department for Education describing the proportion of children currently attending school.
  3. Daily data on the numbers of people getting immunised by age-group and region. These data are derived from the National Immunisation Management Service (NIMS). These data includes all COVID-19 immunisations administered at hospital hubs, local immunisation service sites such as GP practices, and dedicated immunisation centres.

Epidemic summary

Current \(R_t\)

Value of \(R_t\), the average number of secondary infections due to a typical infection today.

Number of infections

Attack rate

The percentage of a given group that has been infected.

By region

By age

Current IFR

Change in infections incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England 0.01 -0.01 0.03
East of England 0.01 -0.04 0.04
East Midlands -0.01 -0.06 0.03
London 0.01 -0.03 0.05
North East -0.01 -0.06 0.04
North West -0.05 -0.10 0.00
South East 0.00 -0.04 0.04
South West 0.01 -0.03 0.05
West Midlands -0.01 -0.05 0.04
Yorkshire and The Humber -0.01 -0.05 0.03

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA 82.28 NA
East of England NA 17.11 NA
East Midlands 71.74 11.40 NA
London NA 20.73 NA
North East 61.40 10.98 NA
North West 14.06 6.87 234.85
South East NA 18.46 NA
South West NA 22.58 NA
West Midlands 93.86 12.77 NA
Yorkshire and The Humber 48.63 12.66 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 73.66 23.49 NA
East of England 136.74 16.49 NA
East Midlands NA 21.76 NA
London 99.82 14.81 NA
North East NA 18.76 NA
North West NA NA NA
South East 175.30 18.23 NA
South West 63.14 13.82 NA
West Midlands NA 17.52 NA
Yorkshire and The Humber NA 23.48 NA

Change in deaths incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England -0.03 -0.04 -0.01
East of England -0.02 -0.05 0.01
East Midlands -0.03 -0.06 0.00
London -0.01 -0.04 0.02
North East -0.04 -0.06 0.00
North West -0.06 -0.07 -0.04
South East -0.02 -0.05 0.01
South West -0.02 -0.04 0.02
West Midlands -0.03 -0.06 0.00
Yorkshire and The Humber -0.04 -0.06 -0.01

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 26.20 18.86 47.16
East of England 32.13 14.93 NA
East Midlands 19.55 11.58 177.80
London 64.18 17.70 NA
North East 18.82 11.06 302.69
North West 11.56 9.10 18.70
South East 28.58 13.65 NA
South West 39.38 15.44 NA
West Midlands 20.62 11.90 1704.93
Yorkshire and The Humber 17.67 11.38 67.43

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA NA NA
East of England NA 61.65 NA
East Midlands NA NA NA
London NA 33.18 NA
North East NA NA NA
North West NA NA NA
South East NA 97.21 NA
South West NA 45.04 NA
West Midlands NA NA NA
Yorkshire and The Humber NA NA NA

Infections and deaths

The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (07 May).

Infection incidence

By region

By age

Cumulative infections

By region

By age

Deaths incidence

By region

By age

Cumulative deaths

By region

By age

IFR

Prob \(R_t > 1\)

The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.

\(R_t\)

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